Zinc in PDB 4zur: Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor, PDB code: 4zur was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.80 / 1.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.990, 120.700, 64.520, 90.00, 97.04, 90.00
R / Rfree (%)	11.4 / 13.6

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor (pdb code 4zur). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor, PDB code: 4zur:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:6.2 occ:1.00 O10 A:7XA404 1.9 8.2 0.8 OD2 A:ASP284 2.0 6.8 1.0 OD1 A:ASP195 2.0 5.0 1.0 O A:HOH512 2.0 3.7 0.1 ND1 A:HIS197 2.1 6.5 1.0 O A:HOH524 2.1 2.0 0.1 N9 A:7XA404 2.7 6.6 0.8 CG A:ASP195 2.7 5.7 1.0 OD2 A:ASP195 2.7 6.0 1.0 O11 A:7XA404 2.9 10.8 0.8 CE1 A:HIS197 2.9 6.5 1.0 CG A:ASP284 2.9 6.8 1.0 H A:HIS197 3.0 6.5 1.0 HE1 A:HIS197 3.0 7.8 1.0 C8 A:7XA404 3.1 8.3 0.8 HB2 A:HIS197 3.1 7.2 1.0 CG A:HIS197 3.2 6.0 1.0 OD1 A:ASP284 3.3 7.1 1.0 HE2 A:HIS158 3.3 8.3 1.0 HA3 A:GLY321 3.4 7.9 1.0 HN9 A:7XA404 3.5 7.9 0.8 CB A:HIS197 3.6 6.0 1.0 HE1 A:TYR323 3.6 8.4 1.0 HH A:TYR323 3.7 9.9 1.0 N A:HIS197 3.8 5.4 1.0 HB3 A:PHE196 3.8 7.3 1.0 H A:PHE196 4.0 6.8 1.0 NE2 A:HIS158 4.1 6.9 1.0 HE1 A:HIS158 4.1 8.4 1.0 NE2 A:HIS197 4.1 6.1 1.0 H A:GLY321 4.2 7.8 1.0 CB A:ASP195 4.2 5.5 1.0 CD2 A:HIS197 4.2 5.9 1.0 CB A:ASP284 4.3 6.0 1.0 CA A:GLY321 4.3 6.6 1.0 N A:PHE196 4.3 5.6 1.0 CA A:HIS197 4.3 5.8 1.0 HB2 A:ASP284 4.4 7.2 1.0 HB3 A:HIS197 4.4 7.2 1.0 CE1 A:HIS158 4.4 7.0 1.0 HB3 A:ASP284 4.5 7.2 1.0 HB3 A:ASP195 4.5 6.6 1.0 C7 A:7XA404 4.5 9.2 0.8 HD2 A:PHE196 4.5 7.6 1.0 CE1 A:TYR323 4.5 7.0 1.0 OH A:TYR323 4.5 8.3 1.0 H A:GLY322 4.6 9.6 1.0 N A:GLY321 4.7 6.5 1.0 CB A:PHE196 4.7 6.1 1.0 HA3 A:GLY282 4.7 8.2 1.0 HB2 A:ASP195 4.7 6.6 1.0 C A:PHE196 4.8 5.6 1.0 H61 A:7XA404 4.8 11.9 0.8 O A:HOH766 4.8 11.1 0.6 H71 A:7XA404 4.8 11.0 0.8 CA A:PHE196 4.8 6.0 1.0 C A:ASP195 4.8 5.4 1.0 NE2 A:HIS159 4.8 7.0 1.0 HE2 A:HIS197 4.9 7.3 1.0 HA2 A:GLY321 4.9 7.9 1.0 CA A:ASP195 4.9 5.5 1.0 HA A:ASP195 4.9 6.6 1.0 C A:GLY321 5.0 6.9 1.0 H62 A:7XA404 5.0 11.9 0.8

Zinc binding site 2 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:6.2 occ:1.00 O10 B:7XA404 1.9 9.8 0.8 OD2 B:ASP284 2.0 5.5 1.0 OD1 B:ASP195 2.0 6.0 1.0 ND1 B:HIS197 2.1 6.2 1.0 O B:HOH526 2.1 5.7 0.1 O B:HOH527 2.2 3.8 0.1 CG B:ASP195 2.7 5.7 1.0 N9 B:7XA404 2.7 6.6 0.8 OD2 B:ASP195 2.7 6.1 1.0 O11 B:7XA404 2.9 10.9 0.8 CE1 B:HIS197 2.9 5.8 1.0 CG B:ASP284 2.9 6.4 1.0 H B:HIS197 3.0 6.5 1.0 HB2 B:HIS197 3.1 6.6 1.0 HE1 B:HIS197 3.1 7.0 1.0 C8 B:7XA404 3.2 8.3 0.8 CG B:HIS197 3.2 5.8 1.0 OD1 B:ASP284 3.3 7.0 1.0 HE2 B:HIS158 3.3 8.1 1.0 HA3 B:GLY321 3.4 8.6 1.0 HN9 B:7XA404 3.5 7.9 0.8 CB B:HIS197 3.6 5.5 1.0 HH B:TYR323 3.7 9.6 1.0 HE2 B:TYR323 3.7 8.7 1.0 N B:HIS197 3.8 5.4 1.0 HB3 B:PHE196 3.8 8.3 1.0 H B:PHE196 4.0 7.4 1.0 HE1 B:HIS158 4.0 8.2 1.0 NE2 B:HIS158 4.0 6.8 1.0 NE2 B:HIS197 4.1 6.1 1.0 H B:GLY321 4.2 8.0 1.0 CB B:ASP195 4.2 5.7 1.0 CD2 B:HIS197 4.2 6.2 1.0 CB B:ASP284 4.2 6.0 1.0 N B:PHE196 4.3 6.2 1.0 CA B:GLY321 4.3 7.2 1.0 CA B:HIS197 4.3 5.6 1.0 HB3 B:HIS197 4.4 6.6 1.0 HB2 B:ASP284 4.4 7.3 1.0 CE1 B:HIS158 4.4 6.8 1.0 HB3 B:ASP284 4.5 7.3 1.0 HD2 B:PHE196 4.5 8.3 1.0 HB3 B:ASP195 4.5 6.8 1.0 OH B:TYR323 4.5 8.0 1.0 CE2 B:TYR323 4.6 7.2 1.0 C7 B:7XA404 4.6 9.2 0.8 H B:GLY322 4.6 9.5 1.0 N B:GLY321 4.7 6.7 1.0 CB B:PHE196 4.7 7.0 1.0 HA3 B:GLY282 4.7 7.7 1.0 HB2 B:ASP195 4.7 6.8 1.0 C B:PHE196 4.8 6.5 1.0 O B:HOH790 4.8 8.4 0.6 C B:ASP195 4.8 6.0 1.0 NE2 B:HIS159 4.8 6.8 1.0 CA B:PHE196 4.8 6.8 1.0 H72 B:7XA404 4.8 11.1 0.8 H61 B:7XA404 4.9 12.8 0.8 HE2 B:HIS197 4.9 7.3 1.0 CA B:ASP195 4.9 5.6 1.0 HA2 B:GLY321 4.9 8.6 1.0 HA B:ASP195 4.9 6.7 1.0 C B:GLY321 5.0 6.9 1.0

C.Decroos, D.W.Christianson. Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry V. 54 4692 2015.
ISSN: ISSN 0006-2960
PubMed: 26200446
DOI: 10.1021/ACS.BIOCHEM.5B00536